sjia abdc8521ea Added debug options for FindClosestHLAWalker ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3549 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-14 17:52:03 +00:00
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alignment	BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.	2010-05-20 14:05:13 +00:00
analyzecovariates	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!).	2010-06-14 16:00:22 +00:00
oneoffprojects	Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!	2010-06-11 21:41:29 +00:00
playground	Added debug options for FindClosestHLAWalker	2010-06-14 17:52:03 +00:00
utils	A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)	2010-06-14 15:54:37 +00:00